Intestinal mucosal morphology was studied in dogs given a new reconstruction procedure following proctocolectomy in which a jejunal segment was interposed between the terminal ileum and the anus to function as a ‘neocolon’. Chronic inflammatory cell infiltration, villous atrophy, and fibrosis of the lamina propria were sought in three different intestinal sites and assigned a severity score. Twenty-four weeks after proctocolectomy, villous atrophy and fibrosis of the lamina propria were noted both in the interposed jejunum (neocolon) (p < 0.05, p < 0.01, respectively) and the terminal ileum (p < 0.05, p < 0.05, respectively). Similar changes were also observed in the proximal jejunum, but a significant difference compared to the preoperative time was not seen. Fibrosis of the lamina propria in the interposed jejunum tended to be more advanced than that in the other two sites. A statistical difference in severity was obtained between the interposed jejunum and the proximal jejunum (p < 0.05). Chronic inflammatory cell infiltration was similar in all sites examined. No obvious evidence of acute inflammation was found at any site examined. These data suggest that chronic morphologic changes inevitably occur at any site in the remaining intestine after proctocolectomy and that an interposed jejunal segment is most severely affected. The new interposition procedure may be effective in reducing the morphologic changes in the terminal ileum because of its proximal displacement.